get_domain_cols = function(){
  c("#f3a683", "#f7d794", "#778beb", "#e77f67", "#cf6a87", "#f19066",
    "#f5cd79", "#546de5", "#e15f41", "#c44569", "#786fa6", "#f8a5c2",
    "#63cdda", "#ea8685", "#596275", "#574b90", "#f78fb3", "#3dc1d3",
    "#e66767", "#303952")
}

get_vcColors = function(alpha = 1, websafe = FALSE, named = TRUE){
  if(websafe){
    col = c("#F44336", "#E91E63", "#9C27B0", "#673AB7", "#3F51B5", "#2196F3",
            "#03A9F4", "#00BCD4", "#009688", "#4CAF50", "#8BC34A", "#CDDC39",
            "#FFEB3B", "#FFC107", "#FF9800", "#FF5722", "#795548", "#9E9E9E",
            "#607D8B")
  }else{
    col = c(RColorBrewer::brewer.pal(11, name = "Paired"), RColorBrewer::brewer.pal(11,name = "Spectral")[1:3],'black', 'violet', 'royalblue', '#7b7060', '#535c68')
    col = grDevices::adjustcolor(col = col, alpha.f = alpha)
  }

  if(named){
    names(col) = names = c('Nonstop_Mutation','Frame_Shift_Del','IGR','Missense_Mutation','Silent','Nonsense_Mutation',
                          'RNA','Splice_Site','Intron','Frame_Shift_Ins','In_Frame_Del','ITD','In_Frame_Ins',
                          'Translation_Start_Site',"Multi_Hit", 'Amp', 'Del', 'Complex_Event', 'pathway')
  }

  col
}

# from http://cell.com/article/S0092867418303027/pdf
get_cell_cols <- function(){
  c(ACC = "#D8B024", BLCA = "#FFDADE", BRCA = "#FF309C", CESC = "#FFBD6E", CHOL = "#006192", COAD = "#7EE5F9", DLBC = "#0093C5",
	ESCA = "#0093C5", GBM = "#D864AC", HNSC = "#89D6B3", KICH = "#FF0712", KIRC = "#FFB9BB", KIRP = "#FF7E82", LAML = "#965B2F",
	LGG = "#EDABCF", LIHC = "#D1D3DF", LUAD = "#DFCFE4", LUSC = "#B296C7", MESO = "#72419C", OV = "#FE8B06", PAAD = "#708DB2",
	PCPC = "#F8CA00", PRAD = "#AC1817", READ = "#D4F0FC", SARC = "#00B8AD", SKCM = "#C1D742", STAD = "#00BCEB", TGCT = "#EC1931",
	THCA = "#FFEB11", THYM = "#E1B79B", UCEC = "#FFE4CC", UCS = "#FF9D00", UVM = "#00A256")
}

# from https://www.cell.com/action/showPdf?pii=S2211-1247%2818%2931564-X
get_col2 <- function(){
  c("#552E89", "#EB7075", "#F8B767", "#DAF0FD", "#FBD3DB", "#A0DDF9", "#F79623", "#CFAD91", "#0D9648", "#EC2029", "#97D1A9",
	"#F8B0B3", "#EC2292", "#D49DC7", "#BE202F", "#DA7E27", "#29ACE2", "#A083BD", "#A083BD", "#FCE2C7", "#127FB7", "#7D1919",
	"#0C4B80", "#CACCDB", "#C2A732", "#6F7DA2", "#D2C4DE", "#18AA9D", "#3954A5", "#F6EE33", "#B2509D", "#E7C51D",
	"#B8D63A", "#673A13")
}

cancer.type.color <- c(BRCA = "#ED2891", GBM = "#B2509E", LGG = "#D49DC7", ACC = "#C1A72F", 
                       PCPG = "#E8C51D", THCA = "#F9ED32", CHOL = "#104A7F", COAD = "#9EDDF9", 
                       ESCA = "#007EB5", LIHC = "#CACCDB", PAAD = "#6E7BA2", READ = "#DAF1FC", 
                       STAD = "#00AEEF", CESC = "#F6B667", OV = "#D97D25", UCEC = "#FBE3C7", 
                       UCS = "#F89420", HNSC = "#97D1A9", UVM = "#009444", LAML = "#754C29", THYM = "#CEAC8F", 
                       DLBC = "#3953A4", SKCM = "#BBD642", SARC = "#00A99D", LUAD = "#D3C3E0", 
                       LUSC = "#A084BD", MESO = "#542C88", BLCA = "#FAD2D9", KICH = "#ED1C24", 
                       KIRC = "#F8AFB3", KIRP = "#EA7075", PRAD = "#7E1918", TGCT = "#BE1E2D")